Volume and surface misalignment in histological space

Q&A Forum Visualisation
#1

Dear all,
I am new to the community, and I am a researcher working on morphological brain complexity estimation. I want to use the amazing resources within the BigBrain project, but I have problems visualizing cortical layer surfaces overlaid with volumes. Specifically, I have been trying to use 3DSlicer and Freeview to visualize “BigBrainRelease.2015/3D_Volumes/Histological_Space/nii/full8_1000um_optbal.nii.gz” with the surface “BigBrainRelease.2015/Layer_Segmentation/3D_Surfaces/PLoSBiology2020/stl/layer0_left_327680.stl.gz” overlaid. The volume and the surface should live in the histology space, but it doesn’t look like it (see the Freeview screenshot below). The same happens when I use the MR image in the histology space “BigBrainRelease.2015/3D_MRI/nii/mri_to_blk_aligned.nii.gz”.

Screenshot 2022-11-28 at 14.20.38
Screenshot 2022-11-28 at 14.20.381920×875 122 KB

Any suggestions are most welcome!
Best,
Chiara

#2

@paulej @lindsayblewis can you help here?

#3

It is my understanding that STL is not a supported medical imaging format (subject:"Re: [Freesurfer] Odd thing about mris_convert? Position changed from freesurfer format to .stl"), and is only intended here for use with 3D printing. Try using the gii format instead, it looks fine to me in freeview:

BigBrainRelease.2015/Layer_Segmentation/3D_Surfaces/PLoSBiology2020/gii/layer0_left_327680.gii.gz

#4

Dear Lindsay,

thanks for your suggestions: it works!

Best,
Chiara